Article Figures & Data

Figures

Genealogical trees under the standard neutral model and hitchhiking model. The branches of the subtree rooted by the node are defined as the major (thick) branches and the rest of the tree is defined as the minor (thin) branches. (A) Balanced tree under the standard neutral model. (B) Unbalanced tree under the standard neutral model. (C) Unbalanced tree under the hitchhiking model when the sample size is small. (D) Unbalanced tree under the hitchhiking model with a large sample size The major part consists of lineages, and the minor part lineages.

Illustrations of possible coalescent event vectors for a sample when and There are possible sequences of coalescent events. The vector elements are ordered according to the order of coalescent events; “” stands for the coalescent event on major branches and “” for the coalescent event on minor branches. Each coalescent event on major branches corresponds to an index where is the number of lineages in the major part right before the coalescent event, and is the number of lineages in the whole tree right before this event.

False positive rate of the tests under (A) population size expansion, (B) bottleneck, (C) the finite island, and (D) the recent population divergence model. DuOG stands for the test when an outgroup is available. DuNoOG represents the test when no outgroup is available. and we assume no recombination within the locus. For population size expansions (E), where and are the current and ancestral effective population size, respectively. For bottlenecks (F), and where is the effective population size during the bottleneck, the duration of the bottleneck. For the finite island model (G), the number of demes is two. We assume that the sample is collected from one deme, and a MD from another. For the divergence model (H), the divergence time of the two demes is generations ago, where is the current effective population size of each deme. We assume two demes with same population size, and the sample is collected from one deme, and a MD from another.

Powers of the tests under positive selection. DuOG stands for the test with outgroup. DuNoOG for the test without outgroup. (A) (B) (C) (D) We assumed that the population size is constant, (or ) and where is the time back to the completion of the selective substitution (in units of generations). The assumed selection coefficient represents strong selection in Drosophila (Li and Stephan 2006). The x-axis is the genetic distance from the selected allele to the examined neutral locus. We assume that there is no recombination within the locus.

Illustration of the effects of misinferred ancestral (upper cases) and derived (lower cases) status of single nucleotide polymorphism. (A) The true case. The open circles represent two mutations occurred on the minor and major branches. (B) The case that the ancestral and derived status of alleles is misinferred. The misinference does not affect the estimation of and since and 1 in both (A) and (B).

Tables

Table 1The presumptive signatures of positive selection on the chromosome 10 of maize

Win start

Win end

Γ

P-value

84,631,154

84,651,154

81

185

94

−1.3858

0.0122

84,633,154

84,653,154

81

198

100

−1.3665

0.0078

84,635,154

84,655,154

81

210

108

−1.4343

0.0096

84,637,154

84,657,154

81

213

112

−1.5171

0.0070

84,639,154

84,659,154

81

234

123

−1.5190

0.0107

84,641,154

84,661,154

81

229

122

−1.5690

0.0095

84,643,154

84,663,154

81

244

131

−1.6007

0.0074

84,645,154

84,665,154

81

225

122

−1.6361

0.0080

84,647,154

84,667,154

81

220

118

−1.5934

0.0089

84,649,154

84,669,154

81

244

128

−1.5128

0.0082

and the length of windows is 20 kb. Win Start: the start position of each window; Win End: the end position of each window; : the number of segregating sites in each window; : the number of segregating sites on minor branches.

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